Effect of base quality on alignment

[rachanajain]

What is the role of read quality in alignment. If say I have 2 sets of fastqs. One of them has reads that are 100bp long and have high quality scores. And another has identical sequences but the sequencing quality is poor, should I expect to see a difference in alignment rates ?

[alexdobin]

Hi @rachanajain

the poorer-quality reads will have lower mapping rates, and also lower mapped length, and higher mismatch rates.

[rachanajain]

Thank you for your reply. Why do we expect mismatch rates to increase when the reads are identical except for base quality.

[alexdobin]

If you have two different FASTQ files, I am not sure I understand how their sequences can be identical. Lowe quality scores usually results in larger error rates.